The crossover hasn't been done in RC track, but a 9V crossing will work just fine, as PF and RC track are physically compatible (the only difference being the lack of conducting metal on PF track, which is a problem only when using 9V motors).
LEGO never produced specific bridges, which makes sense since everyone builds his own. The closest thing would be Heavy hauler, which contains ready-made bridge elements - but that's the upper decoration only, you'd still need to build a sturdy structure under it.
Another reason why LEGO probably never made any is that they'd also need to take sloping into account, and it would mean a set containing way too much track. The Duplo and monorail slopes can be very steep because the trains use gears on a rack, but a regular LEGO train will need a way more gentle slope. Some people recommend no more than 1 plate every track piece; 1 brick is really pushing it (depending on your train), and more is certainly not a good idea. Even with 1 brick every track piece, you'll only get 8 bricks higher every meter. Not a problem if you've got the bricks and track, but it makes sense that LEGO wouldn't produce a full slopes/bridge set.
Sloping by itself isn't required either, as the slope has to be gentle, the existing track will easily accommodate the connections. There you'll certainly need to limit the slope change to no more than one plate per track part. For example, if you really want to have a slope of 1 brick per track, you'll need to start with 1 plate, then only 1 brick (+2 plates) and 2 bricks (+3 plates). Same thing at the top, so if you go to 10 bricks for example, the heights of your pillars will be: ...0, 0, 0, 1 plate, 1 brick, 2 bricks, 3, 4, 5, 6, 7, 8, 9, 9 bricks and 2 plates, 10 bricks, 10, 10, ... Yup, it's long. Note that if you don't care about that, the flex-track piece is very flexible in that regards too.
When LEGO introduced RC track, one of their arguments was that they would be able to do much more fun stuff with track, which they immediately demonstrated with the double-crossover switch, and later with the flex-track, but unfortunately they haven't really followed suit on that topic. Probably trains aren't such a big market for LEGO (that's the reason they stopped 9V to start with).
And you didn't read this from me, but RC track is easier to mod than 9V track...
As for what's possible, keep in mind there are some existing software for track planning. Even LEGO has a basic online one, but for serious stuff you'd probably better use Alban Nanty's BlueBrick. There's also Train Depot Track Designer which hasn't been updated in a long time but may still prove easier to use.